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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgctttgtcatttagattccaatttagtgatgtttttatttacttagtaaataaagttctgaatgagcactcatgtctggaacactaactgtgcag

Basic information

species Zea mays
transcript GRMZM2G064023_T01
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgttta--tgctttg------tcatttag-attccaatttagtgatgtttttat--ttacttagtaaataaagttctgaatgagcactc---atgtctggaacactaactgtgcag
||||| ||||| ||||| |||||||||||||||||||||||| ||||||||||||||||| |||||||||| |||||||||||  ||   ||      | |||||| |  | |||||| |  ||     ||  |    ||||||||  | ||| ||| ||| |||    |     ||    |||| |  ||||
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag

upper sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 18
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgctttgtcatttagat--------------tccaatttagtgatgtttttat--ttacttagtaaataaagttct-gaatgagcactcatgtctggaacactaactgtgcag
||||| ||||| ||||| ||||||||||||||||| |||||| | ||||||||||||||| |||||||||| |||||||||||| || | |   ||| |               || |||||| |  ||   ||||  |    ||| ||||  |  | | ||| ||| ||| | |       | ||||||| ||||
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCGgtatgtttat-ctgtattggttaaacaatctaatgccatgtctaatttaatcttgaacttatgatagagtagcaaatctaactttagaacgagtacttaagaaaacttctctaactgcgcag

upper sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA15G42300.1 (Glycine max), 5'ss of exon 18
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgctt-tgtcatttagattccaatttagtgatgtttttatttacttagtaaataaagttctgaatgagcactcatgtctggaac-actaactgtgcag----
|| || || || ||||||||||||||||| |||||||||||  | |||||| ||| ||| ||| |||| | |  |||||    | ||| | |||  |   ||||| || |   ||  |||   | | || | || ||   || |          |||| |   || | | ||||   |  |    
GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacctg--ttccacttga--aatagttt---tcattttgcaattatttttttagggtgaatttcatctaatgatctattaacatcgtggacag

upper sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
lower sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 18
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgctt-tgtcatttagattccaatttagtgatgtttttatttacttagtaaataaagttctgaatgagcactcatgtctggaac-actaactgtgcag----
|| || || || ||||| |||||||||||||||||||||||  | |||||| | | ||| ||| |||| | |  |||||    | ||| | ||| ||   ||||| || |   ||  |||   | | || | || ||   ||  |  |||   || || |   || | | |||   ||  |    
GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttg--ttccacttga--aatagttt---tcattttgcaattattttttagggtgaat-ctaatctaatgatctattaatattgtggacag

upper sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 17
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgctttgtcatttagattccaatttagtgatgtttttatttacttagtaaataaagttctgaatgagcactcatgtctggaacactaactgtgcag
||||||||||||||||| || ||||||||||| || |||||  | |||||| ||| ||| ||| | |||||| |||| |    | |||    ||  ||  |   |  | ||  || |     ||  ||| ||  || ||   |||     |  |||  | | |                
GTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAGgtaggaac-tacttgtgtatcgaggctttgaccttgttttgctgaatcttggttatta--tagag---tgacattcctttcaaatatag----------------

upper sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgctttgtcatttagattccaatttagtgatgtttttatttacttagtaaataaagt-tctgaatgagcactcatgtctggaacactaactgtgcag
|| |||||||||||||| |||||||||||||||||||| || ||||||||||||| ||| ||| | |||||| |||| |     |     || || |  |  ||      |   |  ||    ||      ||||| | | ||||   |     |                         
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctccttcaagtatca------ttgagccttaggatagcactcaaatataatatctgtgcgttttatag-----------------------

upper sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 18
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgctttgtcatttagattccaatttagtgatgtttttatttacttagtaaataaagttctgaatgagcactcatg--tctggaacactaa---ctgtgcag
|| || ||||| ||||| ||||| |||||||||||||| || ||||||||||| |||||  ||   |||||||||||      | || | |||     |||  ||||  | ||| | || ||||   || | ||||   |  ||  |      | |     ||  |||| |     |  |||||
GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACGgtaaaga-gttctctctcacaatcattataatt-ggagatttcttaatttggctatttaatagtatcttgggtagatggtaaaaatcctttaacaattgatcccttgcag

upper sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
lower sequence: PP1S163_94V6.1 (Physcomitrella patens), 5'ss of exon 16
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgta-tgtttatgctttgtcatttagattccaatttagtgatgtttttatttacttagtaaataaa--gttctgaatgagc--actcatgtctggaacactaactgtgcag
|| || ||||| ||||||||||| |||||||| |||||||| |||||  | |||| ||| ||     ||| || | | ||   |  | ||  | | || | |      |  |     |    ||||   | |   |     |  |  | || |   ||| |||| ||      | | |||||||
GTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTG---AAAGAACAGAAgtgagcagtccttcccttgtaaactattcaattattccactcaggtttagggaatctgttgcctgcaccaagtgggtggacttatgt-tgatttgatgaatgtgcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211314254|gb|FK994154.1|FK994154
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
EST: gi|6020672|gb|AW065480.1|AW065480
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
EST: gi|5847106|gb|AW000185.1|AW000185
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
EST: gi|67022591|gb|CO451340.1|CO451340
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
EST: gi|32859372|gb|CD999053.1|CD999053
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
EST: gi|71450119|gb|DR831169.1|DR831169
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATTTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
EST: gi|4776524|gb|AI665527.1|AI665527
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
EST: gi|76284364|gb|DV023932.1|DV023932
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATTTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
EST: gi|31361873|gb|CD446230.1|CD446230
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATTTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
EST: gi|149082724|gb|EE171942.2|EE171942
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATTTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCGAGAAGCATGGGGATAGGATCCCA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgctttgtcatttagattccaatttagtgatgtttttatttacttagtaaataaagttctgaatgagcactcatgtctggaacactaactgtgcag

- - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC